Impact of interventions
Sam Abbott
2020-02-02
Package
Get linelist
Extract variables of potential interest
## # A tibble: 26,756 x 6
## country city province date_confirmati… travel_history_lo… import_status
## <chr> <chr> <chr> <chr> <chr> <chr>
## 1 China Chaohu Ci… Anhui 22.01.2020 "Wuhan" imported
## 2 China Baohe Dis… Anhui 23.01.2020 "Luzhou Hunan, vi… imported
## 3 China High-Tech… Anhui 23.01.2020 "Yinzhou Hunan, v… imported
## 4 China High-Tech… Anhui 23.01.2020 "" local
## 5 China Feidong C… Anhui 23.01.2020 "Wuhan" imported
## 6 China Lu'an City Anhui 24.01.2020 "" local
## 7 China Fuyang Ci… Anhui 22.01.2020 "Wuhan" imported
## 8 China Huaibei C… Anhui 25.01.2020 "Wuhan" imported
## 9 China Huainan C… Anhui 26.01.2020 "Wuhan" imported
## 10 China Hefei City Anhui 23.01.2020 "Wuhan" imported
## # … with 26,746 more rowsEstimate fraction that are imported
Based on linelist data alone. Only countries with at least 20 total cases present are shown.
Based on linelist data and WH0 sit reps
Summarise and report
| Country | Cases | Fraction imported (linelist only) | Fraction imported (WHO sit reps) |
|---|---|---|---|
| Vietnam | 16 | 0.69 | 0.69 |
| Australia | 27 | 0.87 | 0.48 |
| Kuwait | 56 | 1.00 | 0.46 |
| Malaysia | 24 | 0.65 | 0.46 |
| Bahrain | 47 | 1.00 | 0.43 |
| Thailand | 42 | 0.35 | 0.33 |
| United Arab Emirates | 21 | 0.35 | 0.33 |
| Singapore | 106 | 0.34 | 0.29 |
| United States | 62 | 0.88 | 0.24 |
| Japan | 254 | 0.07 | 0.21 |
| France | 100 | 0.42 | 0.08 |
| Germany | 129 | 0.15 | 0.02 |
| Italy | 1689 | 0.02 | 0.01 |
| South Korea | 4212 | 0.02 | 0.00 |
| Iran | 978 | 0.00 | 0.00 |
Plot cases over time
Wrangle for countries of interest (with at least 40 cases)
Plot curves in countries of interest
## Warning: Removed 9 rows containing missing values (position_stack).
- Save plot
## Saving 7 x 5 in image## Warning: Removed 9 rows containing missing values (position_stack).Get interventions
- Plot overall interventions
## Warning: Missing column names filled in: 'X8' [8]## Parsed with column specification:
## cols(
## date_intervention = col_character(),
## intervention = col_character(),
## social_distancing = col_character(),
## country = col_character(),
## notes = col_character(),
## ref1 = col_character(),
## ref2 = col_character(),
## X8 = col_character()
## )| Intervention | Countries that have implemented |
|---|---|
| Health screening | 5 |
| School closure | 5 |
| Remote working | 4 |
| Travel advisory | 4 |
| Government on alert | 3 |
| Quarantine | 3 |
| Travel restriction | 3 |
| Isolation | 2 |
| Lockdown | 2 |
| Mandatory quarantine | 2 |
| Mass gathering advisory | 2 |
| Mass gathering cancellation | 2 |
| School closure (not related to outbreak) | 2 |
| Social event cancellation | 2 |
| Suspending flights | 2 |
| Travel ban | 2 |
| University closure | 2 |
| Work closure (not related to outbreak) | 2 |
| [Extension] school and work closure | 1 |
| Border checks | 1 |
| Border control | 1 |
| Communciation distancing | 1 |
| Communication distancing | 1 |
| Communication general | 1 |
| Contact tracing | 1 |
| Containment to mitigation | 1 |
| Decontamination | 1 |
| Enhanced care | 1 |
| Entry ban | 1 |
| Government announcement | 1 |
| Healthcare restrictions | 1 |
| Mass gathering ban | 1 |
| Medical surveillance | 1 |
| Prevention measures school | 1 |
| Public information | 1 |
| Raise awareness flights | 1 |
| Raise awareness healthcare staff | 1 |
| Raise awareness public | 1 |
| Reduced shop hours | 1 |
| Resumption public services | 1 |
| School restictions | 1 |
| School restrictions | 1 |
| Social distancing misc | 1 |
| Strengthening primary care response | 1 |
| Supply | 1 |
| Surveillance | 1 |
| Travel advice | 1 |
- Social interventions only
| Intervention | Countries that have implemented |
|---|---|
| School closure | 5 |
| Remote working | 4 |
| Quarantine | 3 |
| Isolation | 2 |
| Lockdown | 2 |
| Mandatory quarantine | 2 |
| Mass gathering advisory | 2 |
| Mass gathering cancellation | 2 |
| School closure (not related to outbreak) | 2 |
| Social event cancellation | 2 |
| University closure | 2 |
| Work closure (not related to outbreak) | 2 |
| [Extension] school and work closure | 1 |
| Communciation distancing | 1 |
| Communication distancing | 1 |
| Contact tracing | 1 |
| Healthcare restrictions | 1 |
| Mass gathering ban | 1 |
| Prevention measures school | 1 |
| Reduced shop hours | 1 |
| School restictions | 1 |
| School restrictions | 1 |
| Social distancing misc | 1 |
| Travel advice | 1 |
| Travel restriction | 1 |
- Non-social interventions
| Intervention | Countries that have implemented |
|---|---|
| Health screening | 5 |
| Travel advisory | 4 |
| Government on alert | 3 |
| Travel restriction | 3 |
| Suspending flights | 2 |
| Travel ban | 2 |
| Border checks | 1 |
| Border control | 1 |
| Communication general | 1 |
| Containment to mitigation | 1 |
| Decontamination | 1 |
| Enhanced care | 1 |
| Entry ban | 1 |
| Government announcement | 1 |
| Medical surveillance | 1 |
| Public information | 1 |
| Raise awareness flights | 1 |
| Raise awareness healthcare staff | 1 |
| Raise awareness public | 1 |
| Resumption public services | 1 |
| Strengthening primary care response | 1 |
| Supply | 1 |
| Surveillance | 1 |
| Travel advice | 1 |
- Plot social interventions
## Warning: Column `country` joining factor and character vector, coercing into
## character vector## Warning: Removed 9 rows containing missing values (position_stack).
## Saving 7 x 5 in image## Warning: Removed 9 rows containing missing values (position_stack).- Plot non-social interventions
## Warning: Column `country` joining factor and character vector, coercing into
## character vector## Warning: Removed 9 rows containing missing values (position_stack).
## Saving 7 x 5 in image## Warning: Removed 9 rows containing missing values (position_stack).